BtaINT0112960 @ bosTau6
Intron Retention
Gene
ENSBTAG00000005947 | PLAU
Description
Bos taurus plasminogen activator, urokinase (PLAU), mRNA. [Source:RefSeq mRNA;Acc:NM_174147]
Coordinates
chr28:29967478-29968056:+
Coord C1 exon
chr28:29967478-29967697
Coord A exon
chr28:29967698-29967907
Coord C2 exon
chr28:29967908-29968056
Length
210 bp
Sequences
Splice sites
5' ss Seq
CATGTATGT
5' ss Score
5.71
3' ss Seq
TCTGACTGATCTCCCCACAGTGA
3' ss Score
9.29
Exon sequences
Seq C1 exon
GAAAAAGTCCCTCCTCTCCTAGGGAGAAAGAAGAGTTCCAATGTGGCCAGAAGGCTCTGAGGCCTCGCTTTAAGATTGTTGGGGGACAGGTCACCAACGCCGAGAACCAGCCTTGGTTTGCAGCCATCTACAGGAGGCATCGAGGAGGCTCCATCACCTACTTGTGTGGTGGCAGCCTCATCAGTCCCTGCTGGGTGGTCAGCGCCACACACTGCTTCAT
Seq A exon
GTATGTTCCTTCTTTCTTGGCCCTGACCCTTCTGCCCAAAGGAATCCCTTCCTCCTTCCCAGCAAAAGATTCTCCTTATTTCTGATCCCTCAGCCTCTCTCTACATGGCCCATGGCCTTGGGGAGAGGTGATGCTCTCAGGTCATTGTGGTGGGGAGGGGAGAGTGACAGGCTCTCACAAGATCAGATTGTCTGACTGATCTCCCCACAG
Seq C2 exon
TGATCACCCAAAGAAGGAGAACTACATTGTCTACTTGGGTCAGTCACGGCTTAACTCCGACACACGTGGGGAGATGCAGTTTGAGGTGGAAAAGCTCATCTTGCATGAGGACTATAGTGCGGAGAGCCTTGCTCACCACAATGATATTG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000005947:ENSBTAT00000007806:7
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.054 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0008921=Trypsin=PU(19.9=64.9)
A:
NA
C2:
PF0008921=Trypsin=FE(20.7=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Chicken
(galGal4)
No conservation detected
Zebrafish
(danRer10)
No conservation detected
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
GCTCTGAGGCCTCGCTTTAAG
R:
AGCAAGGCTCTCCGCACTATA
Band lengths:
300-510
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]